Published online 27 July 2005
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Large-scale structural analysis of the core promoter in mammalian and plant genomes
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University Technologiepark 927, B-9052 Ghent, Belgium
*To whom correspondence should be addressed. Tel: +32 9 331 3807; Fax: +32 9 331 3809; Email: Yves.VandePeer{at}psb.ugent.be
Received March 29, 2005. Revised June 10, 2005. Accepted July 10, 2005.
DNA encodes at least two independent levels of functional information. The first level is for encoding proteins and sequence targets for DNA-binding factors, while the second one is contained in the physical and structural properties of the DNA molecule itself. Although the physical and structural properties are ultimately determined by the nucleotide sequence itself, the cell exploits these properties in a way in which the sequence itself plays no role other than to support or facilitate certain spatial structures. In this work, we focus on these structural properties, comparing them between different organisms and assessing their ability to describe the core promoter. We prove the existence of distinct types of core promoters, based on a clustering of their structural profiles. These results indicate that the structural profiles are much conserved within plants (Arabidopsis and rice) and animals (human and mouse), but differ considerably between plants and animals. Furthermore, we demonstrate that these structural profiles can be an alternative way of describing the core promoter, in addition to more classical motif or IUPAC-based approaches. Using the structural profiles as discriminatory elements to separate promoter regions from non-promoter regions, reliable models can be built to identify core-promoter regions using a strictly computational approach.
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